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Updated: Jan 20, 2026

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
Published on: July 7, 2010
Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function
Xiao-Ou Zhang1, Thomas R Gingeras2, Zhiping Weng1,3
1Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Older Alu elements, transcribed by RNA Polymerase III (Pol III), may act as cell-type-specific enhancers for human genes. This study identifies and maps these crucial Pol III-transcribed Alu elements.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Alu elements are abundant, repetitive transposons in the human genome.
- Identifying and quantifying RNA Polymerase III (Pol III)-transcribed Alu elements is challenging due to their repetitive nature.
- A subset of Alu elements is transcribed by Pol III, while others are part of RNA Polymerase II (Pol II) transcripts.
Purpose of the Study:
- To create a comprehensive atlas of Pol III-transcribed Alu elements.
- To investigate the regulatory roles and epigenetic landscape of these elements.
- To understand the potential exaptation of Alu elements in the human genome.
Main Methods:
- Generated high-resolution, long-genomic-span RAMPAGE data across 155 biosamples with matching RNA-seq data.
- Integrated ChIP-seq data for 10 histone marks and numerous transcription factors.
- Analyzed whole-genome bisulfite sequencing and ChIA-PET data for epigenetic and structural insights.
Main Results:
- Constructed an atlas of 17,249 Pol III-transcribed Alu elements.
- Demonstrated that human-specific Alu elements are transcriptionally repressed.
- Revealed that older, expressed Alu elements may function as cell-type-specific enhancers for nearby protein-coding genes.
Conclusions:
- Older, expressed Alu elements have been exapted by the human host genome.
- These exapted Alu elements can serve as crucial cell-type-specific enhancers.
- This provides new insights into the functional evolution of repetitive elements in humans.
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